diff options
4 files changed, 62 insertions, 0 deletions
diff --git a/pkgs/applications/science/biology/inormalize/default.nix b/pkgs/applications/science/biology/inormalize/default.nix new file mode 100644 index 000000000000..d202db8521cf --- /dev/null +++ b/pkgs/applications/science/biology/inormalize/default.nix @@ -0,0 +1,38 @@ +{ stdenv, fetchFromGitHub, cmake, makeWrapper, + perl, GetoptTabular, MNI-Perllib, + libminc, EBTKS }: + +stdenv.mkDerivation rec { + pname = "inormalize"; + name = "${pname}-1.0.20"; + + src = fetchFromGitHub { + owner = "BIC-MNI"; + repo = pname; + rev = "79cea9cdfe7b99abfd40afda89ab2253b596ad2f"; + sha256 = "1ahqv5q0ljvji99a5q8azjkdf6bgp6nr8lwivkqwqs3jm0k5clq7"; + }; + + patches = [ ./lgmask-interp.patch ./nu_correct_norm-interp.patch ]; + + nativeBuildInputs = [ cmake makeWrapper ]; + buildInputs = [ libminc EBTKS ]; + propagatedBuildInputs = [ perl GetoptTabular MNI-Perllib ]; + + cmakeFlags = [ "-DLIBMINC_DIR=${libminc}/lib/" "-DEBTKS_DIR=${EBTKS}/lib/" ]; + + checkPhase = "ctest --output-on-failure"; # but no tests + + postFixup = '' + for p in $out/bin/*; do + wrapProgram $p --prefix PERL5LIB : $PERL5LIB + done + ''; + + meta = with stdenv.lib; { + homepage = "https://github.com/BIC-MNI/${pname}"; + description = "Program to normalize intensity of MINC files"; + maintainers = with maintainers; [ bcdarwin ]; + platforms = platforms.unix; + }; +} diff --git a/pkgs/applications/science/biology/inormalize/lgmask-interp.patch b/pkgs/applications/science/biology/inormalize/lgmask-interp.patch new file mode 100644 index 000000000000..953bce9a1848 --- /dev/null +++ b/pkgs/applications/science/biology/inormalize/lgmask-interp.patch @@ -0,0 +1,10 @@ +diff --git a/lgmask.in b/lgmask.in +index 17dbe4d..2195d91 100644 +--- a/lgmask.in ++++ b/lgmask.in +@@ -1,4 +1,4 @@ +-#! @PERL@ ++#! /usr/bin/env perl + + #--------------------------------------------------------------------------- + #@COPYRIGHT : diff --git a/pkgs/applications/science/biology/inormalize/nu_correct_norm-interp.patch b/pkgs/applications/science/biology/inormalize/nu_correct_norm-interp.patch new file mode 100644 index 000000000000..75dc46a799ce --- /dev/null +++ b/pkgs/applications/science/biology/inormalize/nu_correct_norm-interp.patch @@ -0,0 +1,10 @@ +diff --git a/nu_correct_norm.in b/nu_correct_norm.in +index 1dc84ac..1bc6235 100644 +--- a/nu_correct_norm.in ++++ b/nu_correct_norm.in +@@ -1,4 +1,4 @@ +-#! @PERL@ ++#! /usr/bin/perl + + #--------------------------------------------------------------------------- + #@COPYRIGHT : diff --git a/pkgs/top-level/all-packages.nix b/pkgs/top-level/all-packages.nix index 51edd6d16e03..cd34788fc39b 100644 --- a/pkgs/top-level/all-packages.nix +++ b/pkgs/top-level/all-packages.nix @@ -19741,6 +19741,10 @@ with pkgs; igv = callPackage ../applications/science/biology/igv { }; + inormalize = callPackage ../applications/science/biology/inormalize { + inherit (perlPackages) GetoptTabular MNI-Perllib; + }; + iv = callPackage ../applications/science/biology/iv { neuron-version = neuron.version; }; |